Germline Genetic NBN Variation and Predisposition to B-cell Acute Lymphoblastic Leukemia in Children

Biallelic mutation in the DNA-damage repair gene NBN is the genetic cause of Nijmegen Breakage Syndrome, which is associated with predisposition to lymphoid malignancies. Heterozygous carriers of germline NBN variants may also be at risk for leukemia development, although this is much less characterized. We systematically examined the frequency of germline NBN variants in pediatric B-ALL and identified 25 putatively damaging NBN coding variants in 50 of 4,183 B-ALL patients. Compared with the frequency of NBN variants in 118,479 gnomAD non-cancer controls we found significant overrepresentation in pediatric B-ALL (p=0.004, OR=1.77). Most B-ALL-risk variants were missense and cluster within the NBN N-terminal domains. Using two functional assays, we verified 14 of 25 variants with severe loss-of-function phenotypes and thus classified these as pathogenic or likely pathogenic. Finally, we found that heterozygous germline NBN variant carriers showed similar survival outcomes relative to those with WT status. Taken together, our findings provide novel insights into the genetic predisposition to B-ALL, the impact of NBN variants on protein function and suggest that heterozygous NBN variant carriers may safely receive B-ALL therapy.